Items where Data Creator is Clark, Taane"
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2009
Almagro-Garcia, J and Clark, T (2009). SnoopCGH. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. http://snoopcgh.sourceforge.net/
2012
Coll, F, Mallard, K, Preston, M, Bentley, S, Parkhill, J, Mcnerney, R, Martin, N and Clark, T (2012). In Silico Spoligotyping. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://web.archive.org/web/20140726124623/http://pathogenseq.lshtm.ac.uk/
Preston, MD, Manske, M, Horner, N, Assefa, S, Campino, S, Auburn, S, Zongo, I, Ouedraogo, J, Nosten, F, Anderson, T and Clark, T (2012). VCF Viewer (VARB). [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://web.archive.org/web/20140726124623/http://pathogenseq.lshtm.ac.uk/
20 August 2012
Cliff, J, Lee, J, Constantinou, N, Cho, J, Clark, TG, Ronacher, K, King, EC, Lukey, PT, Duncan, K, Van Helden, PD, Walzl, G and Dockrell, HM (2012). Tuberculosis Patients Blood Gene Expression Through Treatment. [Data Collection]. ArrayExpress. http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-31348/
Cliff, J, Lee, J, Constantinou, N, Cho, J, Clark, TG, Ronacher, K, King, EC, Lukey, PT, Duncan, K, Van Helden, PD, Walzl, G and Dockrell, HM (2012). Tuberculosis Patients Blood Gene Expression Through Treatment (cured and end-of-treatment patients). [Data Collection]. ArrayExpress. http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-36238/
2014
Coll, F, Mcnerney, R, Guerra-Assunção, JA, Glynn, JR, Perdigão, J, Viveiros, M, Portugal, I, Pain, A, Martin, N and Clark, TG (2014). Data for: "A robust SNP barcode for typing Mycobacterium tuberculosis complex strains". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00000414.
May 2014
Coll, F, Preston, M, Guerra-Assunção, JA, Hill-Cawthorn, G, Harris, D, Perdigão, J, Viveiros, M, Portugal, I, Drobniewski, F, Gagneux, S, Glynn, JR, Pain, A, Parkhill, J, McNerney, R, Martin, N and Clark, T (2014). PolyTB: A web-based resource designed to explore Mycobacterium tuberculosis complex (MTBC) genomic variation at a global scale. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. http://pathogenseq.lshtm.ac.uk/#tuberculosis
2015
Coll, F, Mcnerney, R, Preston, MD, Guerra-assunção, JA, Warry, A, Hill-Cawthorne, G, Mallard, K, Nair, M, Miranda, A, Alves, A, Perdigão, J, Viveiros, M, Portugal, I, Hasan, Z, Hasan, R, Glynn, J, Martin, N, Pain, A and Clark, T (2015). TB Profiler. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. http://tbdr.lshtm.ac.uk/
18 March 2015
Mobegi, V, Duffy, C, Amambua-Ngwa, A, Loua, KM, Laman, E, Nwakanma, DC, MacInnis, B, Aspeling-jones, H, Murray, L, Clark, T, Kwiatkowski, DP and Conway, D (2015). Genome-wide analysis of selection on the malaria parasite Plasmodium falciparum in West African populations of differing infection endemicity: Supplementary data. [Data Collection]. Molecular Biology and Evolution, Oxford Journals. https://doi.org/10.1093/molbev/msu106
26 March 2015
Benavente, E, Coll, F, Furnham, N, Mcnerney, R, Glynn, J, Campino, S, Pain, A, Mohareb, FR and Clark, T (2015). PhyloTrack. [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.82.
15 October 2015
Getachew, S, To, S, Trimarsanto, H, Thriemer, K, Clark, T, Petros, B, Aseffa, A, Price, RN and Auburn, S (2015). Variation in Complexity of Infection and Transmission Stability between Neighbouring Populations of Plasmodium vivax in Southern Ethiopia. [Data Collection]. PLOS ONE. https://doi.org/10.1371/journal.pone.0140780.s005
4 November 2015
Phelan, J, Coll, F, Mcnerney, R, Ascher, DB, Pires, DEV, Furnham, N, Coeck, N, Hill-Cawthorne, GA, Nair, MB, Mallard, K, Ramsay, A, Campino, S, Hibberd, M, Pain, A, Rigouts, L and Clark, T (2015). Whole genome sequences for M.tuberculosis isolates from the TDR strain bank. [Data Collection]. European Nucleotide Archive. http://www.ebi.ac.uk/ena/data/view/PRJEB11653
1 January 2016
Coker, OO, Chaiprasert, A, Ngamphiw, C, Tongsima, S, Regmi, SM, Clark, T, Ong, RTH, Teo, Y, Prammananan, T and Palittapongarnpim, P (2016). Mycobacterium tuberculosis Nonthaburi genotype raw reads. [Data Collection]. National Center for Biotechnology Information. https://www.ncbi.nlm.nih.gov/sra/SRX1094545
5 July 2016
Ansari, HR, Templeton, TJ, Subudhi, AK, Ramaprasad, A, Tang, J, Lu, F, Naeem, R, Hashish, Y, Oguike, MC, Benavente, ED, Clark, TG, Sutherland, CJ, Barnwell, JW, Culleton, R, Cao, J and Pain, A (2016). Genome-scale comparison of expanded gene families in Plasmodium ovale wallikeri and Plasmodium ovale curtisi with Plasmodium malariae and with other Plasmodium species. [Data Collection]. International Journal for Parasitology. https://doi.org/10.1016/j.ijpara.2016.05.009.
8 February 2017
Andreu, N, Phelan, J, de Sessions, PF, Cliff, JM, Clark, T and Hibberd, M (2017). Primary macrophages and J774 cells respond differently to infection with Mycobacterium tuberculosis. [Data Collection]. Gene Expression Omnibus. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE88801
22 September 2017
Diez Benavente, E, Florez de Sessions, P, Moon, RW, Holder, AA, Blackman, MJ, Roper, C, Drakeley, CJ, Pain, A, Sutherland, CJ, Hibberd, ML, Campino, S and Clark, TG (2017). Analysis of nuclear and organellar genomes of Plasmodium knowlesi in humans reveals ancient population structure and recent recombination among host-specific subpopulations. [Data Collection]. Figshare. https://doi.org/10.1371/journal.pgen.1007008
2 May 2018
Sepúlveda, N, Phelan, J, Diez-Benavente, E, Campino, S, Clark, TG, Hopkins, H, Sutherland, C, Drakeley, CJ and Beshir, KB (2018). Global analysis of Plasmodium falciparum histidine-rich protein-2 ( pfhrp2 ) and pfhrp3 gene deletions using whole-genome sequencing data and meta-analysis. [Data Collection]. Infection, Genetics and Evolution. https://doi.org/10.1016/j.meegid.2018.04.039
2 August 2018
Palittapongarnpim, P, Ajawatanawong, P, Viratyosin, W, Smittipat, N, Disratthakit, A, Mahasirimongkol, S, Yanai, H, Yamada, N, Nedsuwan, S, Imasanguan, W, Kantipong, P, Chaiyasirinroje, B, Wongyai, J, Toyo-oka, L, Phelan, J, Parkhill, J, Clark, TG, Hibberd, ML, Ruengchai, W, Palittapongarnpim, P, Juthayothin, T, Tongsima, S and Tokunaga, K (2018). Evidence for Host-Bacterial Co-evolution via Genome Sequence Analysis of 480 Thai Mycobacterium tuberculosis Lineage 1 Isolates. [Data Collection]. Scientific Reports. https://doi.org/10.1038/s41598-018-29986-3
14 August 2018
Sobkowiak, B, Glynn, JR, Houben, Rein M. G. J., Mallard, K, Phelan, JE, Guerra-Assunção, JA, Banda, L, Mzembe, T, Viveiros, M, McNerney, R, Parkhill, J, Crampin, AC and Clark, TG (2018). Additional file 1: of Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.6968636.v1
24 June 2019
Phelan, J, O’Sullivan, DM, Machado, D, Ramos, J, Oppong, YE, Campino, S, O’Grady, J, McNerney, R, Hibberd, ML, Viveiros, M, Huggett, JF and Clark, TG (2019). Additional file 1: of Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.8318861.v1
15 December 2020
Srilohasin, P, Prammananan, T, Faksri, K, Phelan, JE, Suriyaphol, P, Kamolwat, P, Smithtikarn, S, Disratthakit, A, Regmi, SM, Leechawengwongs, M, Twee-Hee Ong, R, Teo, YY, Tongsima, S, Clark, TG and Chaiprasert, A (2020). Genomic evidence supporting the clonal expansion of extensively drug-resistant tuberculosis bacteria belonging to a rare proto-Beijing genotype. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.13378598.v1
11 May 2021
Fuehrer, H, Dombrowski, JG, Barateiro, A, Peixoto, EPM, Barros, André Boler Cláudio da Silva, Souza, RMd, Clark, TG, Campino, S, Wrenger, C, Wunderlich, G, Palmisano, G, Epiphanio, S, Gonçalves, LA and Marinho, CRF (2021). Study database for: "Adverse pregnancy outcomes are associated with Plasmodium vivax malaria in a prospective cohort of women from the Brazilian Amazon". [Data Collection]. PLOS Neglected Tropical Diseases. https://doi.org/10.1371/journal.pntd.0009390.s009
27 June 2021
Spadar, A, Phelan, J, Diez-Benavente, E, Campos, M, Gomez, LF, Mohareb, F, Clark, TG and Campino, S (2021). Data for: "Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus". [Data Collection]. London School of Hygiene & Tropical Medicine, London, United Kingdom. https://doi.org/10.17037/DATA.00002482.
10 November 2021
Damilola R. Oresegun, Peter Thorpe, Benavente, E, Campino, S, Fauzi Muh, Moon, RW, Clark, T and Cox-Singh, J (2021). Getting close to nature – Plasmodium knowlesi reference genome sequences from contemporary clinical isolates. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.5598263
24 December 2021
Gibson, AJ, Passmore, IJ, Faulkner, V, Xia, D, Nobeli, I, Stiens, J, Willcocks, S, Clark, TG, Sobkowiak, B, Werling, D, Villarreal-Ramos, B, Wren, BW and Kendall, SL (2021). Table_1_Probing Differences in Gene Essentiality Between the Human and Animal Adapted Lineages of the Mycobacterium tuberculosis Complex Using TnSeq.XLSX. [Data Collection]. Frontiers. https://doi.org/10.3389/fvets.2021.760717.s002
17 February 2022
Eccleston, RC, Manko, E, Campino, S, Clark, TG and Furnham, N (2022). A computational method for predicting the most likely evolutionary trajectories in the stepwise accumulation of resistance mutations. [Data Collection]. Zenodo. https://doi.org/10.5281/zenodo.6122329
23 May 2022
Oresegun, DR, Thorpe, P, Benavente, ED, Campino, S, Muh, F, Moon, RW, Clark, TG and Cox-Singh, J (2022). De Novo Assembly of Plasmodium knowlesi Genomes From Clinical Samples Explains the Counterintuitive Intrachromosomal Organization of Variant SICAvar and kir Multiple Gene Family Members. [Data Collection]. Frontiers. https://doi.org/10.3389/fgene.2022.855052.s001
13 April 2023
Spadar, A, Perdigão, J, Campino, S and Clark, TG (2023). Additional file 2 of Large-scale genomic analysis of global Klebsiella pneumoniae plasmids reveals multiple simultaneous clusters of carbapenem-resistant hypervirulent strains. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.22611932.v1
13 August 2024
Spadar, A, Phelan, J, Clark, TG and Campino, S (2024). Additional file 1 of Large-scale reference-free analysis of flavivirus sequences in Aedes aegypti whole genome DNA sequencing data. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.26608764.v1
Spadar, A, Phelan, JE, Clark, TG and Campino, S (2024). Additional file 3 of Large-scale reference-free analysis of flavivirus sequences in Aedes aegypti whole genome DNA sequencing data. [Data Collection]. Figshare. https://doi.org/10.6084/m9.figshare.26608770.v1